micromanager-samples

Python code samples for Micro-manager image acquisition system

Micromanager project provides broad opportunity for constructing sophisticated image acquisition protocols (e.g. in microscopy). So it becomes possible to overreach vendor software limitation and realize your inherent researcher's freedom as far as possible.

Unfortunately, micromanager documentation lacks for detailed examples. It is not easy to understand the hardware capabilities and API logic. I hope those samples will be helpful in your journey, especially for live video acquisition.

Available samples

• Getting list of available properties and their allowed values
• Video grabbing with opencv highgui
• Efficient frame conversion with Numpy (rgb32 to rgb, bgr)
• Qt GUI (property browser)
• OpenGL context for efficient video output

Setup

Windows

Install Micromanager from official website and add C:\Program Files\Micro-Manager-1.4 to PYTHONPATH system variable. After that you can simple import micromanager's core:

import MMCorePy

Linux

I made Archlinux PKGBUILD.

See test snippet at the end of the PKGBUILD.

Issues

Memory requirements not adequate

2014-02-11T14:36:41.328125 p:612 t:2300 [LOG] Error occurred. Device BaumerOptronic. Failed to initialize circular buffer - memory requirements not adequate.
Traceback (most recent call last):[Decode error - output not utf-8]
    mmc.startContinuousSequenceAcquisition(1)
  File "C:\Program Files\Micro-Manager-1.4\MMCorePy.py", line 4956, in startContinuousSequenceAcquisition
    return _MMCorePy.CMMCore_startContinuousSequenceAcquisition(self, *args)
MMCorePy.CMMError: Failed to initialize circular buffer - memory requirements not adequate.

Solution: Just increase circular buffer size (60 megabytes works fine for me). According with mailing list 600-800-1200 MB for circular buffer is normal.

mmc.setCircularBufferMemoryFootprint(60)

Circular buffer is empty

mmc.popNextImage() and mmc.getLastImage() both raises an exception while circular buffer is empty.

Solution: Check buffer for image count.

if mmc.getRemainingImageCount() > 0:
    rgb32 = mmc.popNextImage()

Snippets

def rgb32asrgb(rgb32):
    """View RGB32 as RGB array (no copy, very fast).

    low memory address    ---->      high memory address
    | pixel | pixel | pixel | pixel | pixel | pixel |...
    |-------|-------|-------|-------|-------|-------|...
    |B|G|R|A|B|G|R|A|B|G|R|A|B|G|R|A|B|G|R|A|B|G|R|A|...
    http://avisynth.nl/index.php/RGB32
    """
    return rgb32.view(dtype=np.uint8).reshape(
        rgb32.shape[0], rgb32.shape[1], 4)[...,2::-1]

Further reading

• Micro-Manager python library
• Immunopy - an Micro-manager based application (python image processing with Qt, OpenCV, OpenGL, OpenCL)